Ocean Modeling Discussion

fagundesmo

Hi everyone,

Thank you!! I realized my mistake after you mentioned that it was related to metadata and get_data.F.

Best,
Matheus

fagundesmo

Hi everyone, I am working on adding some processes into biofennel, in order to do that I wanted to practice in something simple like hypoxia_srm. The hypoxia_srm requires 3 names r espiration, idResR, ResRate. The respiration is in ana_respiration.h, get_data.F, hypoxia_srm.h, set_data.F, varinfo ...

fagundesmo

Dear all, I am trying to run biofennel + ROMS in COAWST and I get the following error: TIME-STEP YYYY-MM-DD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME C => (i,j,k) Cu Cv Cw Max Speed 0 2015-05-01 00:00:00.00 0.000000E+00 6.377852E+01 6.377852E+01 5.692375E+08 (000,000,00) 0.000000E+00 ...

fagundesmo

Hi Arnaud,

That is amazing, thank you so much!! And I guess didn't look close enough in bio_fennel.in and I am sorry for that!

Best,
Matheus

fagundesmo

Hi everyone, I have looked and could not find a topic related to this, and therefore, I am posting to see if anyone knows whether or not ROMS has a way to add climatology data for BioFennel model. For instance, if I wanted to add climatology for phytoplankton. Is it as simple as turning on ...

fagundesmo

Hi John,

I updated and the error still persists. I will post my files there.

Thank you,
Matheus

fagundesmo

Hi all (sorry in advance my post isn't strictly about ROMS only), In order to make the full coupling (WRF+SWAN+ROMS) I am taking baby steps and trying to see if the models are working properly by themselves and coupled. As of right now, I am trying to couple only SWAN+WRF to see if they would work ...

fagundesmo

Hi Wilkin,

I didn't know that!!! Ok, now the values make sense when I make that shift in my time data.

Thank you a lot,

Matheus

fagundesmo

Hi Giannis,

Thank you a lot for your answer. One more time really helpful.

Cheers,

Matheus

fagundesmo

Hi Giannis, Thank you a lot for your input. I am indeed getting the data from (https://cds.climate.copernicus.eu) but only every 6 hours. Do you know if the values are shifted by 6 hours? Because I have noticed that the peak of swrad is around 18hrs in the data but it's actually supposed to be ...

fagundesmo

Hi all, I am using BULK FLUX and for some reason the way it's showing on ROMS print is not what I am forcing with (see attached lwrad.ps and swrad.ps). The same way I interpolated vwind, uwind, Tair, and Pair I interpolated swrad and lwrad. And as you can see from my output.txt my swrad and lwrad ...

fagundesmo

I would like to point it out that I was able to "fix" by modifying the following in the diag.F (coawst/ROMS/nonlinear/): ! ! Local variable declarations. ! #ifdef BIOLOGY integer :: ibt, itrc #endif integer :: NSUB, i, ispace, j, k, trd integer :: my_max_Ci, my_max_Cj, my_max_Ck #ifdef DISTRIBUTE ...

fagundesmo

Hi all, I was wondering if you could help me out with this issue. I also have posted on the COAWST community but I couldn't attach all the log files and here the community is more active. I am trying to run parts of my model and see if everything works to make sure once I put all together they will ...

fagundesmo

Hey Rintei, First, I am glad you figured it out the problem with salt and temp fields. Secondly, about the tides we would normally create a file with tides only and I don't recall you attaching any tide files so I don't know. I use the matlab files create_roms_tides.m and roms_tide_forc_file.m ...

fagundesmo

Hey Rintei, Again this is all based on trial and error (Kate said that to me once ahah). I looked at your IC file and salinity and temperature are also kinda messed up. For example, figures 1 and 2 are from your IC file and 3 from my file (I'm kinda person that needs to visualize my data that's why ...

fagundesmo

Hi, I was checking your zeta for initial condition and I saw values of -1444 m and max value of 10 m. In my humble opinion as ROMS user, I think you might have not masked properly your land and you should check the region where zeta is 10 m, maybe? I am using HYCOM as well and my model is running ...

fagundesmo

Did you add climatology for SST? If not, I would add climatological monthly data for temperature and give it a try. I did that and my results were better. Also, don't forget it's a model and you are comparing with a reanalysis, and therefore, you cannot expect D_sst approximately 0.

Cheers,
Matheus

fagundesmo

Hi Kate thank you again for the prompt response, the CFL is around 0.5 now but I was wondering if setting u component as zero would not be causing the model to blow up as well. If so, should I mask all the zeros that I created or instead of zeros should I substitute for NaN values. Do you think my ...

fagundesmo

Dear roms users, I am running an Idealized case where only the Northern Boundary is opened and the East and West bdry are periodic. However, the model keeps blowing up even though max CFL is between 1 and 0.5. For my case I only don't consider zonal component and all size of detritus in the Northern ...

fagundesmo

hmm,

so if I had 20 yrs of ocean BRY and had all those years merged in one file that could create a problem to ROMS (US version)? If so, that could explain many things in my outputs ahahha.

fagundesmo

May I suggest you merging all files in one?

fagundesmo

Hi John,

thank you for the information, I'll try this here.

Best Regards,

Matheus

fagundesmo

Hi all,

I have faced the same issue but now that I have the net radiation how should I set my .h file so ROMS can read and use it properly?

Best Regards,

Matheus

fagundesmo

I am not sure I'm the best person to give advices since I'm only an undergraduate student but what I did was I took the function to interpolate from z to sigma levels from pyroms and the horizontal interpolation I did using another function and it worked. The ocean_grd I had some trouble with the ...

fagundesmo

I would still play with the timestep. Just because your Courant number based on the initial conditions is less than one, you're not out of the woods. In fact, I don't think 0.83 is out of the woods. Plus, as soon as things start evolving, your forcing, etc. could lead to larger currents than are in ...

fagundesmo

kate wrote:If all the NaNs are in the land mask, you shouldn't see it in the GET_XXX reports like that. You need to clean the Nans out of your input files.

Hi Kate,

I have fixed that in python since I'm still doing the benchmark I'm still waiting for the output.

Thank you,

fagundesmo

Hi wilkin and Helios, I have fixed the NAN problem and now I'm playing with the courant number. Although, I have a max courant number 0.83 it keeps blowing up, I am trying to play with my DT in order to keep my courant number equals to 0.83 and my barotropic time step equals 24 sec. Since, it keeps ...

fagundesmo

Hi Kate,

ok, I'll try it here. Thank you.

fagundesmo

Dear all, my model is blowing up and, therefore, I was wondering if it has anything to do with ubar and vbar having min and max as NAN values. If so, how could I fix this problem since I've checked my ubar e vbar and both have values except in the borders which are masked with NAN values. Model ...

fagundesmo

Hi Fernando,

it will seem a dumb question but have you interpolated first the temp data to your grid?

Matheus

fagundesmo

Hi Fernando, this error is more related to python. If you quickly take a look you'll see that your HYCOM data domain is bigger than your grid/mask_rho maybe. I am not sure what domain has the shape (117,124), but try to re-run this command and always make the command name_of_your_array.shape() to ...

fagundesmo

Hi yadusharma, I had the same problem actually, but for making your grid you don't need to use it (I guess), at least I didn't use it. If you want to interpolate the data to your domain you can give it a try on Trond's package (https://github.com/trondkr/romstools) or using the function (import mpl ...

fagundesmo

Hi yadusharma, I have tried to use pyroms, octant and etc for my preprocessing data and, also, to generate my grid. The thing that I did,(with Kate's help), was installing pyroms in my laptop. Pyroms is a complete package where you can generate your grid and your input data. Octant package is an ...

fagundesmo

Hi Kate,

thank you for your explanation it helped me a lot.

Best Regards,

Matheus

fagundesmo

Hi all, I am starting doing my inputs to my experiment I have a question that I would like the opinion of the ROMS users. Would be a good idea if I created my oceanic and atmospheric forcing from the same reanalysis? For instance, NCEP-CFSR. On the other hand, if I am using one reanalysis to my ...

fagundesmo

Dear Hetland, I am trying to use your python script to make my river. Therefore, I would like to know how your tarbert_landing.npy looks like. Because I have stuck in the line where it asks for the river_jd. I have pasted below a piece of how my data. May you please give me some help? Thank you in ...

fagundesmo

There may be a couple of issues here, the first is that scatteredInterpolant only takes datatype double (real or complex) so your solution will avoid that error. But there may still be a problem with your u_tpxo72.nc file - the version of that file that I have has the variables URe and UIm (the ...

fagundesmo

I think I did it. Could all confirm whether I changed right or not? I added the following lines:

xx=double(x(:,:));
yy=double(y(:,:));
zz=double(z(:,:));
F=scatteredInterpolant(xx(m),yy(m),zz(m),'nearest');
z=F(xx,yy);
F=griddedInterpolant(xx',yy',zz');

fagundesmo

Dear all, I am trying TPX02ROMS version 3.2 to generate tides input to my area. However, I have had some issues while using it. These are the errors I am getting: 'Extracting ' 'M2' ' amplitudes' 'Extracting ' 'M2' ' u components' Error using scatteredInterpolant The input points must be a double ...

fagundesmo

Hi,

thank you a lot. Have a nice day.

Matheus

fagundesmo

Hi Saaed,

I was wondering whether I could smooth my bathymetry using octant or I had to make by hand. Could you help me out?

Cheers,

Matheus

fagundesmo

Did you also install the netcdf-fortran package? --flibs refers to the fortran libraries while --libs refers to the C libraries. They are different. What you added into LIBS has the wrong syntax, sorry. Hi Kate again, I have set my NC_CONFIG (now at this time I think correctly): NC_CONFIG= "/home ...

fagundesmo

It looks like you are missing netcdf. Did you install it? nc-config is not on your path - it is looking for that. You should also check to see if "nc-config --flibs" gives a reasonable reply. If not, edit the makefile to use nf-config instead. It is strange because I did install all libs needed to ...

fagundesmo

Hi Kate, I have been trying to use Octant and pygridgen unsuccessfully, though. Since, I am newer regarding ROMS and making grid to ROMS I am looking for something that I could start with using python. Considering, I have seen many posts related to pyroms and you have helped a lot everybody with ...

fagundesmo

Hi all, I am learning how to make a simple grid to the Equator using pygridgen tool. Thus, it is normal that some error come up sometime so that it has shown me an error which I cannot find out what is wrong, hahaha. Hence, I was wondering if someone would help me. this is my code I have gotten ...

fagundesmo

Hi Saeed, It works fine now :). However, I have noticed that in its newer version from github, Hetland has removed _csa from the setup and _init_.py files. So at the end, I mixed both versions hahaha, and now I can import octant.csa with no problem at all. Also, I built nn,csa, and so on, using its ...

fagundesmo

Hi, It seems the 'libcsa' is not in this directory '/home/fagundes/libsmodels/Grid/lib'. As a test, would you please copy all the libs (.a and .so) files into your ~/.local/lib/ and complie the octant once again. Saeed. Hi, I have compiled octant changing csa's path in csa.py (following these ...

fagundesmo

Hi moghimi, I have fixed this issue as you said. However, now I can't import octant.csa. Even though, I installed nn, gridgen, csa, and gridutils in the same path. When I tried to import octant.csa, I got this error: OSError Traceback (most recent call last) <ipython-input-6-6b2d83a1f717> in ...

fagundesmo

Hi again, I guess, you either need to find the location of the library and change the path to this location inside the code (e.g. here octant.__path__[0] and other places based on the error message)and do python setup install again, or make a symbulic link to that library into your usr/local/lib or ...

fagundesmo

Hi, I have used Octant however I learn it more by looking at the source code and run commands interactively by Ipython. If you have specific question I will be happy to answer/help. - Saeed. Hi, May you help me to install octant correctly in my ubuntu system? It seems I installed nn, csa, gridutils ...

fagundesmo

Hi,

I have been struggling to install successfully pyroms, may you help how to install correctly under ubuntu 14.10 (64 bits)??

Thank you in advance,

Matheus

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